Mass Effect: Reconstruction
by bionaknight
Summary: Utilizing the body of the Shepard Clone from the Citadel DLC, Commander Shepard regains physical form after choosing to control the Reapers. This story shows the fallout from the choices Shepard made over the course of the game, the effect conquering the Reapers has on the Galaxy, and leads up to what will hopefully be my next story set in this universe.
1. Mass Effect: Reconstruction: Chapter 1

MASS EFFECT RECONSTRUCTION

Shepard staggered across the ruined battlefield. His armor, now several panels of burnt, twisted metal, clung to him uncomfortably. A trio of husks clambered over some debris just before Shepard put a single Carnifex round into each of them. As he approached the beam, a marauder leapt out from behind a burning tank, firing a blast into his shoulder. Ignoring the pain, Shepard took careful aim and fired, destroying the Turian husk's head in a single shot. He continued forward, stumbling into the beam that led to the Citadel. The world around him turned to stars for a brief, uncomfortable minute, until he was flung from a conduit into a dark, corpse-filled tunnel.

"Shepard, are you there?" His comm crackled to life as Anderson's voice came through. Shepard stumbled to his feet.

"Yeah. But I don't think we came out in the same place. Where are you?"

"I'm in some sort of tunnel. Reminds me of your description of the Collector base."

Shepard shuddered at the memory. "Makes sense."

"You don't think they're building a Reaper in here, do you?" The old admiral asked, nervously.

"Sure," the commander managed to say through the pain of his wounds. "They round them up on Earth, then bring them here for processing." He staggered from the corridor, ignoring the Keeper poring over the bodies lining the room.

"Goddamn abomination. Where are you now?"

Shepard took in his surroundings. Huge metal plates shifted along the walkway he now dragged himself across.

"I think I'm in some sort of chasm."

"Okay, I think I know where you are, I'm not too far off-wait, I see a terminal. Just going to investig-"

The comm dissolved into static.

"Anderson? Anderson, respond! Damn it."

He slowly marched up a long ramp that led to a wide chamber. Electricity crackled across the ceiling as he approached. Anderson stood by a large terminal. As Shepard approached, he turned stiltedly around to face him, with panic in his eyes.

"Shepard! I...I can't..."

Shepard, startled, tried to step back, only to find he couldn't. A whispering noise flooded his ears as a familiar voice spoke from behind him.

"I underestimated you, Shepard."

The Illusive Man, his skin marred with glowing blue circuitry, strode into the room.

Shepard almost doubled over in agony, but found himself unable to move.

"What have-augh!" He could barely speak through the splitting pain in his skull and chest.

"I warned you. Control is the means to survival. Control of the Reapers...and of you, if necessary."

Shepard tried his best to seem unfazed. 

"Controlling me...is a lot different than controlling a Reaper." said the wounded soldier, inbetween gasps for breath.

The Illusive Man let out a chuckle. "Have a little faith.

He started pacing across the room. "When humanity discovered the Mass Relays, when we learned there was more to the Galaxy than we imagined...there were those who thought the Relays should be destroyed. Those who were scared of what we might find, terrified of what we might let in. But look at what humanity has achieved! Since that discovery, we've advanced more than the past 10,000 years combined! And the Reapers will do the same for us again, a thousand fold! But only if we can harness their ability to control."

Shepard's arm raised up against his will, aiming his weapon at Anderson.

"Bullshit," the admiral muttered. "We destroy them, or they destroy us."

"And waste this opportunity? Never!" The Illusive Man cried.

"You're playing with things you don't understand, with power you shouldn't be able to use." Shepard argued.

"I...don't believe that." The Cerberus leader didn't sound as confident, all of a sudden. "If we can control it, why shouldn't it be ours?"

"Because...we're not ready." Shepard said this as calmly as he could.

"No. This is how humanity must evolve."

"No...there's always...another way..."

"I've dedicated my life to studying the Reapers, and I know with certainty; the Crucible will allow me to control them."

"And then what?" Shepard was getting desperate and running out of time.

"Look at the power they wield! Look at what they can do!" The Illusive Man clenched his fist, and Shepard shot Anderson in the gut.

Shepard gazed in astonishment, shaking his head. "I see what they did to you."

"I took what I wanted from them! Made it my own! This isn't about me or you, this is bigger than all of us!"

"Don't listen to him!" Anderson was pleading now.

"And who will you listen to? The old soldier, set in his ways, only able to see the world down the barrel of a gun? What if controlling the Reapers is the answer?"

"And what if you're wrong? What if you can't control the Reapers?"

"But I can!" The Cerberus leader was clearly exasperated.

"Are you willing to bet humanity's existence on it? Let us go, and we can do the rest."

"I...can't do that, Commander."

Anderson chuckled. "Of course you can't. They own you now."

"No! I'm in control! Nobody's telling me what to do! The two of you, so self-righteous. You think this kind of power comes easily? There are sacrifices!"

"You've sacrificed...too much." Shepard couldn't look his foe in the eye.

"You're wrong! The Crucible can control them, I know it can!"

Shepard was enraged. "You know only what the Reapers fed you! You've failed, you bastard. You belong to them now!"

"No!" The Illusive Man grabbed Anderson's pistol, and forced the Admiral to his knees. "You're the one who's failed!"

The indoctrinated Illusive Man, now focusing on Anderson, momentarily weakened his control on Shepard. It was more than enough. The Commander pulled the trigger, watching as his opponent staggered back before falling to his knees, a shocked look on his face. Shepard staggered to the control panel and opened the station's arms.

"There it is...Earth." The fallen leader stared at the blue planet as he bled out. "I wish you could see it as I do, Shepard. It's so...perfect." He closed his eyes for the last time as the glowing blue circuitry in his skin went dark.

Shepard staggered to where Anderson was sitting and rested next to him.

[ABOARD AN ALLIANCE DREADNOUGHT]

"Holy shit. He did it."

Hackett watched as the arms of the Citadel opened.

"Shield Fleet, get the Crucible docked."

A division of dreadnoughts began to escort the superweapon into the Citadel. It docked slowly, as electricity crackled between the two monolithic structures. Everyone in Sword and Shield Fleets held their breath, watching anxiously as the Crucible primed itself, until finally...it didn't fire. Hackett, desperate to try something, anything, double checked the schematics before finally calling on the Hero of the Citadel once more.

[ON THE CITADEL]

"Shepard, are you there?"

The Commander staggered to his feet before falling again, Anderson's last words thundering in his ears. _I'm proud of you_...

"What do you need me to do?"

"The Crucible isn't firing. Nothing's wrong here, it has to be on your end."

Shepard, half dead, crawled towards the panel.

"I'm not sure...I don't know how to..."

The Commander dropped to the ground, his eyes closed. The ground shifted beneath him as he lost consciousness.

[ON THE CRUCIBLE]

"Wake up."

The noise of many voices speaking at once roused Shepard from his brief slumber.

"You have come far."

Shepard stared in confusion. The strange voice was coming from a hologram, shaped in the image of the child who died on Earth. It felt like a lifetime ago, instead of a few months.

"I need to defeat the Reapers," he asked the child. "Do you know how I can do that?"

"That depends on how."

[EARTH SPACE]

Hackett watched helplessly as a Reaper crushed a ship with its clawed legs. He couldn't believe they had come this far to lose. A beam of energy fired from a nearby Reaper capital ship cleaved a Turian cruiser in half, even as Geth fighters futilely swarmed it. The Quarian fleet rained enough fire to eliminate a nearby Reaper destroyer, but it was only one of many. He saw how hopeless the fight was, and closed his eyes, waiting for it to end.

[ON THE CRUCIBLE]

Shepard sat next to the hologram. To his right, was a power conduit. Destroying it would bring about the deaths of the Reapers. It was what he had set out to do. But the cost would be great. In front of him was a large beam of energy, the Crucible's main core. Should he enter it, his energy would be joined with it, and spread across the galaxy, merging synthetic and organic life and bringing about an era of peace , but against the will of all life. To his left were two handles, crackling with energy. Should he put his hands on them, his body would die, allowing his psyche to be uploaded into each Reaper, erasing what they were and making them extensions of his will. The Illusive Man had been right all this time: The Reapers could be used after all. But he wouldn't be able to be human anymore. He would be immortal, the undying mind of the Reapers. Unless...

Turning to the Starchild, he asked: "Would the Keepers obey me, as well?" 

"Not directly, but you could direct them with Reaper signals."

"But they would do as I instruct."

"That is correct."

He marched to the handles, placing his hands on them and letting their energy flow into his body. He nearly staggered from them, but he grasped them firmly in his hands. As the Starchild faded away, his skin started to darken and blister as he remembered those who had helped him through this.

Anderson.

Thane.

Mordin.

Legion.

Tali.

_Tali_. He closed his eyes, as the pain surged through him. He felt his flesh begin to burn away, his mind leaving his body, and thought to himself:

_I'll see them again. I'll see _her _again._

His body was reduced to ashes, and the Crucible fired.

As ships fled the system, a pulse of blue energy surged forwards.

[ON THE NORMANDY]

Joker hurriedly flung holographic warning signals aside. Garrus watched sadly, putting his hand on his shoulder.

"Joker, listen. We need to go."

The pilot knew he was right.

"Damn it."

The ship turned around and flew towards the Relay, racing against the blast of blue energy that followed them. They fired through the device as the pulse caught up to it.

The blast tailed them as they raced through the stars. A hole in the blast began to open up, and Joker saw his opportunity. Frantically working the controls, he flew in reverse, passing through the void as it closed around the ship. Energy flowed around the ship as the void closed. Nearly losing control, Joker skirted the gravity well of a jungle world before turning back towards Earth.

[SHEPARD'S CONSCIOUSNESS]

Shepard felt the anguish of the minds of each Reaper as they were eradicated, and felt his consciousness flood into them. He could see through the eyes of every Reaper and every Husk, and order them to do as he wished. He moved them from the surface of Earth, and watched as the galaxy cheered. Only one Reaper resisted. The pulse had reached Harbinger, and its cries lasted longer than the others.

_**I DO NOT UNDERSTAND! I CANNOT FAIL! SHEPPAAAAAAAAARD!**_

The first Reaper screamed in anguish, and its thoughts were no more. Stepping mentally into the body of Harbinger, Shepard flew into the atmosphere. _So this is how EDI feels._

The Crucible's energy fired from Relay to Relay, destroying them in a pulse of energy that encompassed every system before moving to its next target. In moments, every Reaper in the galaxy was his to command.

[ON AN ALLIANCE DREADNOUGHT]

Hackett collapsed into a chair. The Crucible worked. The Reapers were fleeing Earth, and the galaxy was safe. An alert sounded in the CIC: they were being hailed. By Harbinger. Dubiously, Hackett answered, and heard a familiar voice:

"This is Commander Shepard. I'm in control of the Reaper forces. The war is over, Admiral. We have peace."

"Shepard? Is that...you?"

"Yeah. Harbinger, along with every Reaper and Husk in the Galaxy, is dead, more or less. Their psyches are gone, now their minds are just conduits I use to command them. My own body was destroyed, but...I'm working on it."

"You've done well, Commander."

"Thank you, sir. Any word on the Normandy?"

"They're returning now. They nearly crashed, but they made it out intact. One hell of a pilot you have there."

"I'll tell him you said that when I see him, sir."

[ON THE CITADEL, 3 DAYS LATER]

The Keepers were excellent servants. As Shepard supervised through a Husk that had found its way onto the Citadel, the Second Lazarus Project neared completion. Ironically, he had Cerberus to thank for his resurrection yet again. Without the clone they had made in case the real Shepard needed a kidney, the only way to interact physically with his crew would be to permanently use a Husk. _Not the best way to meet up with Tali again_, he thought to himself. It was also fortunate that enough medical equipment was aboard the Citadel to set up this lab, with a few Reaper-made upgrades. The clone was all but resurrected in just a couple of days, although Shepard had been extremely careful to leave the brain dead. After installing Reaper implants into the dormant mind of his clone, Shepard prepared himself for the upload. In a moment, he began the process. Soon, all of his psyche, everything that had been uploaded to the Crucible, was installed to those implants. Once his consciousness had flooded in, he staggered to his feet and paced around the room.

It had been some time since he was in a body that wasn't either extremely agile or several kilometers tall. But he could still control the Reapers while using his new form. As he threw on some new clothes, he broke two Destroyers off from the main reconstruction group on the Relay to assist the rebuilding of a nearby Mars colony, and sent a group of Brutes to go get more supplies at a construction site on Thessia. He was in the body of all Reaper forces simultaneously, as though his cloned form was his hand and the Reapers were his fingers. But he could still switch to primary control of any one Reaper, with his bodies either still under direct control or simply obeying mental orders.

As he headed for the Presidium, he saw the Normandy approach drydock. With a smile on his face, he glanced at his reflection in a cracked window. He looked completely normal, although his normally grey-blue eyes had a small but definite cyan glow to them, like a smaller-scale version of the glowing blue eyes that had replaced the Reaper's malevolent red ones when he seized control of them. After adjusting his jacket, he walked off towards Bay D-24. It was time to rejoin his friends.

[PART 1 END, STAY TUNED FOR PART 2]


	2. Mass Effect: Reconstruction: Chapter 2

[MASS EFFECT: RECONSTRUCTION]

The Normandy slipped quietly into the Docking Bay. The crew disembarked slowly, taking in the abandoned station as they walked into the desolate chamber. Tali was the first one off, followed by Garrus, then Kaidan led the rest of the crew aboard. As they approached the elevator, its doors slid open, revealing a familiar form.

"Shepard!" Tali raced to the elevator and into the Commander's arms. After a few moments, Shepard greeted Garrus and the rest of the crew.

"You don't look that bad for a man who's just been to hell and back, Shepard." Garrus said.

"And you look just the same as always." Shepard said, slyly.

"That bad, huh?" Garrus replied, jokingly.

"We've been through a lot, Shepard." Kaidan said with a grin. "But I knew that if we made it this far, a little Reaper invasion couldn't stop you."

"Thanks, Kaidan. You did a fine job yourself. I'm sure you'll make Admiral in no time."

"I certainly hope not." The Major shuddered at the thought. "Me? No way I'd let myself take an easy job like that."

"Don't count yourself out yet," James joked. "You know how the brass gets with promotions. Do one little heroic thing and suddenly you're watching the action from a comfy CIC in some dreadnought."

"Mind explaining how that's a bad thing?" Cortez muttered under his breath. The marine simply ignored him and rolled his eyes.

"I'll admit, Commander, I am...impressed." Javik had been awestruck at what had been accomplished by Shepard's Reapers ever since Hackett had briefed him. "I'm not quite sure I can call you 'primitive' anymore, but I am honored to call you 'friend'."

"Don't start going soft on us, Javik." Garrus quipped.

"I said I can't call the _Commander_ primitive." Javik replied. "I hold no such reservations about you."

"It's good that you survived, Shepard." Liara looked visibly relieved. "I didn't want all my hard work recovering your body to be for nothing, after all." She cracked a feeble smile.

"You thought you worked hard to help him? I flew him all around the galaxy for years! Who else was going to write me up for a commendation?" Joker said, though he was just as relieved as Liara did, despite his brave front.

Shepard smiled. "It's great to see everyone again. Now come on, let's get back to the ship. I've seen enough of this place for a while."

"I couldn't agree more." Tali said quietly as she followed him and the crew back to their ship.

[THE NORMANDY, CREW DECK, MEMORIAL WALL]

Shepard placed the last plaque on the wall.

_Adm. David Anderson_.

He couldn't believe he was gone. The man had been his mentor for years. He had stood up for him, believed in him when nobody else would.

_Have a good rest, sir_, Shepard thought to himself._ You've earned it._

He looked at the names of all of the good men and women who had died under his command. He still remembered Gabriella "Gabby" Daniels, the young engineer who worked so diligently down in Engineering, melted down and used to fuel a Proto-Reaper. And Yeoman Kelly Chambers, who had served as his personal assistant for a long time. She wasn't a soldier, she had never been in combat, and yet her life was taken. Charles Pressly, the navigator on the original Normandy who went down with his ship. Mordin, his friend and ally who died righting an ancient wrong. Thane Krios, who perished saving a Council that had done nothing for him. Legion, the Geth unit who sacrificed himself to build a future for his people. Ashley Williams, who overcame her prejudices and died on Virmire, fighting alongside Salarian soldiers.

All this death, all this sacrifice, and why was Shepard among those who still lived? He doubted himself sometimes. He didn't know if he could have done things differently. If maybe, some of these people might still be alive if he had walked a different path. But then, he looked around the room, and saw the survivors who stood with him. Garrus Vakarian. Jeff "Joker" Moreau. Liara T'Soni. Kaidan Alenko. Tali'Zorah Vas Normandy. They had been with him since this war began. He saw newer faces, too. James Vega. Steve Cortez. Samantha Traynor. EDI. Javik. There may have been death, but there were still survivors. There may have been loss, but there was still hope. Shepard stole a glance at Tali. He knew she felt the same way he did. They both had led people into war. They both knew the toll commanding could take. They embraced, and knew that not all was lost. The Normandy was docked on an Earth that was still turning, that had fallen once but was rebuilding. The dead would not be forgotten, but life would continue. And that gave those sacrifices purpose. And Shepard knew that those he mourned wouldn't have it any other way.

[CITADEL, COUNCIL CHAMBERS. 4 WEEKS LATER]

The Council had grown a bit in size in recent times. With Hackett now having assumed humanity's seat, a vote to give the non-council races that participated in the war positions had passed unanimously. Admiral Zaal'Koris Vas Qwib-Qwib had been elected to the position of Quarian councilor, although he insisted on a name change. Now, Councilor Zaal'Koris Vas Rannoch sat amongst them, serving as the representative for both the Quarians and the Geth, who had formed a united government on their shared homeworld. Beside him was Councilor Bakara, the Krogan queen that had been granted a seat thanks to Urdnot Wrex's relentless lobbying. The six politicians sat in the tower of the newly-refurbished Citadel, locked in debate. A bored Shepard watched idly, flanked by Tali and Garrus.

"All I'm saying is that we need to proceed with caution." The Salarian councilor anxiously ran his tongue across his lips. Shepard smiled to himself as he recalled Javik's mention of their former traits. _They used to lick their eyes_. Valern continued to speak. "The Reapers-"

"Are no longer a threat," Hackett interrupted. "Shepard has seen to that. He's a war hero, the Reapers couldn't be in better hands."

"Agreed." It was Sparatus, the Turian councilor who spoke this time. "You read the report. The Reapers are under Shepard's direct control."

"But can Shepard be trusted?"

The commander was annoyed now. "I'm standing right here, _Councilor_."

"We made the mistake of distrusting him before, Valern." Tevos, the Asari councilor replied sternly. "His Reapers have almost rebuilt Thessia from ruins. If that isn't proof he stands with us, I don't know what is. He has our support in any crisis."

"Not to mention all he's done for us on his own. He came to our aid on Menae when nobody else would. Not even your fleets, Salarian." Sparatus rose from his seat. "Shepard has full Turian endorsement. If you stand against him, you stand against _us_."

The Council had been going over the Salarian's position for weeks. Their refusal to provide more than a token amount of aid during the Reaper War had left them devastated. Even though the newly-controlled Reapers had recently finished rebuilding Sur'Kesh, Valern's people had petitioned to force Shepard to shut down and destroy the Reapers. The rest of the galaxy had some very vocal objections to this idea, as the advancements that the Reapers had brought about had already saved countless lives and outfitted soldiers with powerful new technology. Things had reached a boiling point, and the Council was in a last-ditch effort to avert a full-blown war.

"I concur with Councilor Sparatus. Shepard worked with Mordin Solus, a _Salarian_ doctor and hero, to cure the Genophage, not to mention how he personally rescued me from a Reaper assault." Bakara, ever the politician, emphasized Mordin's race in an effort to appeal to Valern. "The Krogans stand at his side."

"As do the Quarians and Geth." Zaal'Koris, usually reserved, spoke up. "He ended a three century-long war and gave us our homeworld back. Now we've almost rebuilt it with his help. The people of Rannoch grant Shepard our full support."

"And of course, Alliance support is unquestioning. A conflict would be over as soon as it begins, Valern. Don't let your people go through with this." Hackett pleaded.

The Salarian councilor swallowed audibly. "I don't have a choice. The dalatrass has spoken. I have to obey her demands. She left me with only one option if I could not convince you." He rose shakily to his feet.

"The Salarian people hereby secede from the Council. All Salarian forces will return to the Sur'Kesh system in five hours. You have this time to make the necessary transfers to ensure all Council forces have been removed from our ships." He closed his eyes. "I'm sorry."

"No," Hackett replied. "I am." Everyone knew how this conflict would end. Valern took one final look at the beautiful silver halls of the tower as he marched to the elevator. As the doors of the lift that would take him to his private shuttle closed, he looked down and shed a single tear.

[RANNOCH, ONE WEEK AFTER SALARIAN SECESSION]

Tali felt the wind against her face as she watched Rannoch rise from its ashes. It was certainly a peculiar sight. A Geth Prime held a steel column in place as a Quarian engineer fused it into a building's foundation. An army of Husks with supplies on their backs crawled up a massive tower to where a team of Quarian and Geth workers waited, idly talking and laughing. Brutes marched through the streets with entire sections of walls upon their backs, as Banshees levitated panels into place with their biotics for Geth drones to weld into place. Meanwhile, a Reaper Destroyer loomed over a huge portion of the rising metropolis, welding entire buildings together with technology that formerly ended thousands of lives. A _Sovereign_-class ship hovered in the sky, shuttling Husks across the planet with its troop transports. The newly-minted Admiral Kaidan Alenko had also sent Alliance freighters to help supply the workers.

Shepard approached her from behind. "Hey."

"Hey." Tali was still getting used to seeing the world without a transparent wall between her and her environment. Like the rest of her people, masks were no longer required to survive. The Geth had seen to that. They still wore their suits, however. They had become a part of their culture.

The unlikely couple watched the reconstruction around them from their balcony. They lived in an expansive house they had constructed in the very spot Tali had chosen when they had arrived on Rannoch, the spot where they had been married. They overlooked the water, with some of the countless cities of Rannoch on either side of the coast. Their own house still had a respectable amount of untouched beach and a well-kept, grassy yard.

"It's all happening pretty quickly, isn't it?" Shepard said, as he willed a Harvester to grab a shipment of supplies in its claws. The dragon-like creature flew past with its bounty moments later.

"I never thought I'd see the Quarians and the Geth get along. Seeing them rebuild together? With the help of the _Reapers_? It's unbelievable." Tali watched from the distance as a Geth guard chatted amiably with a Quarian worker, as though they were old friends.

"Back on Earth," Shepard said quietly, "I thought I'd never see you again. Seeing that ship leave with you on it was heartbreaking for me. But my will kept me going. My will to have shot at having a peaceful life with you. And I'm overjoyed that I could survive to see this moment."

There was silence for a while, as the two quietly watched the world around them change.

"It was horrible for me, too." Tali said sadly. "I was scared that you would die in that battlefield. But at the same time, I knew you would survive. And I knew this day would come."

The pair found comfort in each other's arms as a galaxy pulled itself back together around them. They knew a war with the Salarians was coming. They knew blood would be shed. But they also knew that they had each other. And in that moment, that was all that mattered.

[TO BE CONTINUED]


End file.
